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Estimating causal effects with machine learning: A guide for ecologists

Suchinta Arif

Published 2025 in Methods in Ecology and Evolution

ABSTRACT

In ecology, there is a growing need to move beyond correlations to uncovering causal effects from observational data. With the parallel increase in big data and machine learning algorithms, the opportunity now exists to benefit from causal machine learning methodologies. This paper presents an accessible overview of four causal machine learning methods, double machine learning (DML), targeted maximum likelihood estimation (TMLE), deep instrumental variables (Deep IV) and causal forests, that can be applied across ecological contexts. DML and TMLE leverage machine learning to estimate causal effects in the presence of known confounders. Deep IV offers a robust solution for addressing unmeasured confounding or bidirectional relationships by pairing valid instruments with deep neural networks. Causal forests uncover heterogeneity in causal effects, shedding light on context‐dependent ecological responses. Adding these causal machine learning techniques to an ecologist's broader causal toolkit will increase the options researchers have for estimating causal relationships, particularly when dealing with complex and large‐scale observational data.

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